User: raf4

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raf420
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r***@cumc.columbia.edu

Posts by raf4

<prev • 23 results • page 1 of 3 • next >
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Comment: A: Error message with Voom with blocked design matrix
... Dear Gordon. I am sorry I confused "warning" for "error". Thank for answering my question. duplicateCorrelation worked just fine. Best wishes, Rich ...
written 9 weeks ago by raf420 • updated 9 weeks ago by Gordon Smyth34k
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Comment: C: Error message with Voom with blocked design matrix
... Dear Aaron, Thank you. I kept my note short to fit in the character limit. Gordon answered my question below. Best wishes, Rich ...
written 9 weeks ago by raf420 • updated 9 weeks ago by Gordon Smyth34k
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Error message with Voom with blocked design matrix
... Dear List, I have encountered an error message in running Voom with weights with a blocked design matrix using what I hope to be a correct implementation of a method that Gordon Smyth told me about which I found to work well with microarrays. Briefly,     Here is the target file: ...
limma voom blocked design written 9 weeks ago by raf420 • updated 9 weeks ago by Gordon Smyth34k
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Minimum in Voomplot
... Dear List, I am using Voom and the Mean variance trend plot, has a  pronounced minimum. https://imgur.com/cgeNtmt Is this a cause for concern? Relevant code: > library(limma) > library(edgeR) > library(org.Mm.eg.db) > targets<-readTargets("targets.txt") > a1<-read.table("a ...
limma voom written 5 months ago by raf420 • updated 5 months ago by Ryan C. Thompson6.8k
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should subgroups of comparisons be analyzed separately in Limma
... Dear Bioconductor, I have a fluidigm (or other array) experiment which consists of 4 groups: A, B, C, and D. The experimentalist I am helping wants to compare B to A and D to C, but not B to D or B to C, etc. Do I 1. Run all 4 groups together in Limma and then analyze the individual contrasts ...
limma design matrix written 7 months ago by raf420 • updated 7 months ago by Gavin Kelly550
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Answer: A: discrepancy between genes corresponding to gene ontology terms in org.Mm.eg.db a
... Jim, Got it! I thought that downloading org.Mm.eg.db_3.4.0 fresh would be sufficient. I have not updated Bioconductor/R because I have a technical problem with my mac which forces me to reboot frequently. Once that is solved (probably by reinstalling the OS). I will update R/Bioconductor.   Th ...
written 9 months ago by raf420
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Comment: C: discrepancy between genes corresponding to gene ontology terms in org.Mm.eg.db a
... Jim, Thank you, as always but I still am not getting all the genes (I am still on R 3.3.3 because there is an intermittent  problem with permissions on my mac which I want to solve before I update. Should that make a difference). > select(org.Mm.eg.db,keys="GO:0044339",column="SYMBOL",keytype= ...
written 9 months ago by raf420
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discrepancy between genes corresponding to gene ontology terms in org.Mm.eg.db and in AMIGO
... Dear Bioconductor, I find fewer genes for a given GO term in mouse with the org.Mm.eg.db than with teh online AMIGO server. I am wondering if the difference is due to delays in updating org.Mm.eg.db, or for some other reason. Here is my R session  library(AnnotationDbi) > library(org.Mm.eg.db) ...
gene ontology written 9 months ago by raf420
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Comment: C: Subject: Strange glitch in Voom curve resulting from batch effects
... Steve and Gordon, When the reads were aligned with the same algorithm, the glitch disappeared. Thanks and best wishes, Rich ...
written 13 months ago by raf420
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Comment: C: Problem running featurecounts in Rsubread on GFF file
... I believe I found part of the problem. I should  not have used the patched sequence. I am currently downloading ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/vertebrate_mammalian/Homo_sapiens/all_assembly_versions/GCA_000001405.15_GRCh38/seqs_for_alignment_pipelines.ucsc_ids/ GCA_000001405.15_GRCh38 ...
written 13 months ago by raf420

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